| mkFunction4DirectFit {CalciOMatic} | R Documentation |
The function mkFunction4DirectFit returns a function
prediciting the exponential time course of fluorescence transients at
two wavelengths (including background fluorescence). The function, the
arguments of which depends on the value of type, can be passed
to the nls formula, for a direct fit
mkFunction4DirectFit(type = "mono", nb_B = 5, transients = 1,
alphamethod = TRUE, SQRT = TRUE)
type |
a character string (either "mono" or "bi"),
specifying which type of exponential decay should be considered |
nb_B |
the number of background measurements performed at each wavelength |
transients |
a vector of integers, specifying the numbers of the
transients to fit (determines the names of the calcium dynamics
parameters (log_Ca0_1, log_Ca0_2, ...)) |
alphamethod |
a logical value. Set to TRUE (respectively
FALSE) to include alpha (respectively B_T) in
the output function formals |
SQRT |
a logical value. Set to TRUE (the default value) to return the square root of the fluorescence signals |
A function, the arguments of which depend on the value of type,
alphamethod and transients. The list below describes all
possible arguments:
t |
the times at which the fluorescence values are expected (in s) |
tOn |
the time of the fluorescence jump (in s) |
adu_B_340 |
the background fluorescence measurement(s) at 340 nm |
adu_340 |
the fluorescence transient(s) at 340 nm |
adu_B_380 |
the background fluorescence measurement(s) at 380 nm |
adu_380 |
the fluorescence transient(s) at 380 nm |
T_340 |
the exposure time at 340 nm |
T_380 |
the exposure time at 380 nm |
P |
the number of pixels of the ROI |
P_B |
the number of pixels of the background region |
log_Ca0_1 |
the logarithm of the Ca^2+ baseline of the first transient |
log_dCa_1 |
the logarithm of the Ca^2+ jump of the first transient |
log_tau_1 |
the logarithm of the Ca^2+ time constant of the first transient |
mu_1 |
the real number (between -Inf and +Inf)
defining the relative weight of the fast and slow time constants of
the Ca^2+ biexponential decay (if type is set to
"bi"). The weight of the fast time constant is given by
exp(mu)/(1+exp(mu)) |
log_dtau_1 |
the logarithm of the dtau defining
the slow time constant of the Ca^2+ biexponential
decay (if type is set to TRUE"bi"). This slow time
constant is given by tau_s=tau+dtau |
log_phi |
the logarithm of the experiment-specific amplitude coefficient |
log_S_B_340 |
the logarithm of the background fluorescence at 340 nm |
log_S_B_380 |
the logarithm of the background fluorescence at 380 nm |
log_R_min |
the logarithm of the minimum ratiometric measurement observable |
log_R_max |
the logarithm of the maximum ratiometric measurement observable |
log_K_eff |
the logarithm of the effective Fura dissociation constant in the cell (in muM) |
log_K_d |
the logarithm of the Fura dissociation constant (in muM) |
alpha |
the isocoefficient. Present only if alphamethod is
set to TRUE. In this case, B_T is replaced with
adu_340/(T_340*P) - adu_B_340/(T_340*P_B) +
alpha * (adu_380/(T_380*P) - adu_B_380/(T_380*P_B)) in the
fluorescence model |
B_T |
the total concentration of the dye in the cell. Present
only if alphamethod is set to FALSE |
Sebastien Joucla sebastien.joucla@parisdescartes.fr
## Parameters of the biexponential calcium transient
tOn <- 1
Time <- seq(0,12,length.out=160)
Ca0 <- 0.10
dCa <- 0.25
tau <- 1.5
mu <- 0
dtau <- 10
## Calibrated parameters
R_min <- 0.136
R_max <- 2.701
K_eff <- 3.637
K_d <- 0.583
## Experiment-specific parameters
B_T <- 100.0
T_340 <- 0.015
T_380 <- 0.006
P <- 200
P_B <- 200
phi <- 2
S_B_340 <- 30
S_B_380 <- 80
## Define a function for fluorescence transients based on
## a monoexponential calcium concentration time course
Fluo_bi_fct <- mkFunction4DirectFit(type = "bi",
nb_B = 5,
transients = 1,
alphamethod = FALSE,
SQRT = TRUE)
## Create the fluorescence transients
Time <- matrix(Time, nrow=1, dimnames=list("1",NULL))
names(tOn) <- "1"
Fluo_bi <- Fluo_bi_fct(t = Time, tOn = tOn,
T_340 = T_340, T_380 = T_380,
P = P, P_B = P_B,
log_Ca0_1 = log(Ca0),
log_dCa_1 = log(dCa),
log_tau_1 = log(tau),
mu_1 = mu,
log_dtau_1 = log(dtau),
log_phi = log(phi),
log_S_B_340 = log(S_B_340),
log_S_B_380 = log(S_B_380),
log_R_min = log(R_min), log_R_max = log(R_max),
log_K_eff = log(K_eff), log_K_d = log(K_d),
B_T = B_T)